B3GALNT2

Chr 1AR

beta-1,3-N-acetylgalactosaminyltransferase 2

Also known as: B3GalNAc-T2, MDDGA11

NCBI Gene: 148789ENSG00000162885UniProt: Q8NCR0

This gene encodes a member of the glycosyltransferase 31 family. The encoded protein synthesizes GalNAc:beta-1,3GlcNAc, a novel carbohydrate structure, on N- and O-glycans. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Mar 2013]

Primary Disease Associations & Inheritance

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 11MIM #615181
AR
658
ClinVar variants
114
Pathogenic / LP
0.00
pLI score
1
Active trials
Clinical Summary— B3GALNT2
🧬
Gene-Disease Validity (ClinGen)
muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
114 Pathogenic / Likely Pathogenic· 265 VUS of 658 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.84LOEUF
pLI 0.000
Z-score 2.20
OE 0.55 (0.36–0.84)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.95Z-score
OE missense 0.84 (0.75–0.93)
222 obs / 265.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.55 (0.36–0.84)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.84 (0.75–0.93)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.91
0≤1.21.6
LoF obs/exp: 15 / 27.4Missense obs/exp: 222 / 265.6Syn Z: 0.72

ClinVar Variant Classifications

658 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic89
Likely Pathogenic25
VUS265
Likely Benign250
Benign19
Conflicting10
89
Pathogenic
25
Likely Pathogenic
265
VUS
250
Likely Benign
19
Benign
10
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
23
0
66
0
89
Likely Pathogenic
14
4
7
0
25
VUS
9
199
55
2
265
Likely Benign
2
4
99
145
250
Benign
0
3
15
1
19
Conflicting
—10
Total48210242148658

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

B3GALNT2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

B3GALNT2-related muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A

definitive
ARLoss Of FunctionAbsent Gene Product
Dev. DisordersEye
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 11

MIM #615181

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Genetic variations and clinical spectrum of dystroglycanopathy in a large cohort of Chinese patients.
Song D et al.·Clin Genet
2021Cohort
Congenital muscular dystrophies in the UK population: Clinical and molecular spectrum of a large cohort diagnosed over a 12-year period.
Sframeli M et al.·Neuromuscul Disord
2017Cohort
Pathogenic mechanisms and clinical insights into B3GALNT2-related alpha-dystroglycanopathies.
Fu X et al.·J Neuromuscul Dis
2025Functional
B3GALNT2-Related Dystroglycanopathy: Expansion of the Phenotype with Novel Mutation Associated with Muscle-Eye-Brain Disease, Walker-Warburg Syndrome, Epileptic Encephalopathy-West Syndrome, and Sensorineural Hearing Loss.
Al Dhaibani MA et al.·Neuropediatrics
2018Review
Unique clinical presentations and follow-up outcomes from experience with congenital disorders of glycosylation: PMM2-PGM1-DPAGT1-MPI-POMT2-B3GALNT2-DPM1-SRD5A3-CDG.
Yoldas Celik M et al.·J Pediatr Endocrinol Metab
2023Natural history
Expanding the Phenotype of B3GALNT2-Related Disorders.
D'haenens E et al.·Genes (Basel)
2022Case report
Mutations in B3GALNT2 cause congenital muscular dystrophy and hypoglycosylation of α-dystroglycan.
Stevens E et al.·Am J Hum Genet
2013
Prenatal diagnosis of Walker-Warburg syndrome due to compound mutations in the B3GALNT2 gene.
Wang P et al.·J Gene Med
2022
[Genetic analysis of a Chinese family affected with α-dystroglycanopathy due to variant of B3GALNT2 gene].
Zeng L et al.·Zhonghua Yi Xue Yi Chuan Xue Za Zhi
2023
B3GALNT2 is a gene associated with congenital muscular dystrophy with brain malformations.
Hedberg C et al.·Eur J Hum Genet
2014Case report
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Compound heterozygous B3GALNT2 mutations in a fetus with encephalocele: A case report.
Ling D et al.·Clin Case Rep
2024🔓 Open AccessCase report
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Muscular Dystrophy

Clinical Trial Readiness for the Dystroglycanopathies

RECRUITING
NCT00313677Katherine MathewsStarted 2006-04

External Resources

Links to major genomics databases and tools